An evo-devo geek's scientific meanderings

transitional forms

Damn, I said I wasn’t going to talk about the Moroccan helicoplacoid-on-stalk, but it’s just so. Bloody. Amazing.

Here it is in its full glory, from the supplementary figures of Smith and Zamora (2013). Left is a cast of a young specimen, right is the authors’ reconstruction of the adult creature:

So… the thing is a transitional form all right. It’s got a little stalk and cup like eocrinoids, built with a rather irregular arrangement of mineralised plates. On top of that it has a spiral body like helicoplacoids. It has ambulacra, the “rays” with porous plates where the tube feet that characterise living echinoderms can come out. This photo of the underside of a starfish is a pretty nice illustration of ambulacra (the white regions with little holes) and tube feet:

Even more interestingly, the new beastie (christened Helicocystis moroccoensis by the authors) seems to have five of them, like modern echinoderms (and a lot of extinct types, including eocrinoids). Helicoplacoids do have ambulacra, but only three or a single Y-shaped one, depending on interpetation.

Again unlike (one interpretation of) helicoplacoids but like modern echinoderms, the mouth of Helicocystis is right at the stalkless end. It’s also surrounded by an arrangement of skeletal plates that resembles more “conventional” echinoderms and has no equivalent in helicoplacoids proper. It’s about as neat a transitional form as you could hope for.

The question is which way the transition goes. It could be that the familiar five-rayed echinoderms are derived from a helicoplacoid-like ancestor, going through something like this guy. Or it could be that helicoplacoids are actually weird even for echinoderms, and their ancestors were more conventional stalked, five-armed beasties that lost their proper echinoderm shapes via something like Helicocystis.

Smith and Zamora actually did a phylogenetic analysis, but it’s not that helpful IMO. The tree in the paper is very pretty, and it says Helicocystis is the next branch after helicoplacoids on the path leading to “proper” echinoderms. The tree in the supplementary figures actually has measures of statistical support on it – which pretty confidently put Helicoplacus, Helicocystis, and a bunch of less weird echinoderms, together.

However, the relationships within that group are, shall we say, a little bit fluid. Granted, I come from a more sequency background and don’t often have to deal with morphology-based trees or parsimony as the method of analysis – but I’d definitely view a 56% bootstrap support with a big dose of scepticism, and this is the number they got for the hypothesis that Helicocystis is more closely related to “proper” echinoderms than to Helicoplacus. The other measure they display doesn’t make me any more confident about the relationship.

(I find it kind of amazing they got any resolution at all in that tree – with only 17 characters, some of which aren’t applicable to all species, and only nine species to begin with… yeah. The whole phylogenetic analysis is far from ideal even if it’s the best they could think of.)

So, based on that tree, the phylogenetic hypothesis they present is, at this point, just a plausible hypothesis. That doesn’t lessen the value of Helicocystis, though. The creature is still a damn neat transitional form – we just can’t be terribly sure which way the transition went.

There’s some interesting speculation in the paper about developmental evolution (yay!). Smith and Zamora point out that the spirally bit in Helicocystis looks like a complete helicoplacoid; the stalk and cup are kind of tacked onto that. The tissues of most modern echinoderm adults come from two different places: regular old tissues of the larva, and a special set of cells set aside for adult-making purposes*. So Smith and Zamora hypothesise that the two-part body of Helicocystis marks the point where this dual origin appeared. (Or, if they’re wrong about the phylogeny, the point where proto-helicoplacoids lost it?)

There’s also another interesting bit of evo-devo speculation (mixed with a bit of “eco”) about the stalk. Full-grown Helicocystis have pretty small stalks compared both to their own young and more typical stalked echinoderms. The authors wonder if this is because stalks for attachment originally functioned to help young echinoderms settle in a comfortable place, and only later became important for adults. I’m not sure how much sense that actually makes, and of course we only have a single species of Helicocystis to go by, but hey, ideas are fun.

Helicocystis has a random weird quirk as well, in that its spirals curl the opposite way to every proper helicoplacoid. That sort of variation happens even within species (e.g. in snail shells), but isn’t it a weird coincidence that such a unique creature should also twist the wrong way?

One thing is for sure: this beast is made of pure, distilled awesome. I think we should make a new Archaeopteryx out of it. Invertebrates need their evolutionary icons, too!

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*And that’s a nice reminder for me, because I thought they basically threw away the larva. Apparently I need a refresher on echinoderm development. Or just a reminder that not all echinoderms are sea urchins. The funny thing is a couple of years ago I actually specifically read and puzzled over literature discussing what comes from where in various echinderms…

Hah, I open my Google Reader (damn you, Google, why do you have to kill it??? >_<), expecting to find maybe a handful of new articles since my last login, and instead getting both Nature and Science in one big heap of awesome. The latest from the Big Two are quite a treat!

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By now, of course, the internet is abuzz with the news of all those four-winged birdies from China (Zheng et al., 2013). I’m a sucker for anything with feathers anywhere, plus these guys are telling us in no uncertain terms that four-wingedness is not just some weird dromaeosaur/troodontid quirk but an important stage in bird evolution. Super-cool.

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Then there is that Cambrian acorn worm from the good old Burgess Shale (Caron et al., 2013). It’s described to be like modern acorn worms in most respects, except it apparently lived in a tube. Living in tubes is something that pterobranchs, a poorly known group related to acorn worms do today. The Burgess Shale fossils (along with previous molecular data) suggest that pterobranchs, which are tiny, tentacled creatures living in colonies, are descendants rather than cousins of the larger, tentacle-less and solitary acorn worms. This has all kinds of implications for all kinds of common ancestors…

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Third, a group used a protein from silica-based sponge skeletons to create unusually bendy calcareous rods (Natalio et al., 2013). Calcite, the mineral that makes up limestone, is not normally known for its flexibility, but the sponge protein helps tiny crystals of it assemble into a structure that bends rather than breaks. Biominerals would just be ordinary rocks without the organic stuff in them, and this is a beautiful demonstration of what those organic molecules are capable of!

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And finally, Japanese biologists think they know where the extra wings of ancient insects went (Ohde et al., 2013). Today, most winged insects have two pairs of wings, one pair on the second thoracic segment and another on the third. But closer to their origin, they had wing-like outgrowths all the way down the thorax and abdomen. Ohde et al. propose that these wing homologues didn’t just disappear – they were instead modified into other structures. Their screwing with Hox gene activity in mealworm beetles transformed some of the parts on normally wingless segments into somewhat messed up wings. What’s more, the normal development of the same bits resembles that of wings and relies on some of the same master genes. It’s a lot like bithorax mutant flies with four wings (normal flies only have two, the hindwings being replaced by balancing organs), except no modern insect has wings where these victims of genetic wizardry grew them. The team encourage people to start looking for remnants of lost wings in other insects…

Gods, this is what I’m faced with all the time. Someone needs to tell me how proper science bloggers pick articles to discuss, because I just get my RSS alerts, start squeeing, and end up not writing about anything because damn, I WANT TO WRITE ABOUT EVERYTHING!

I give up. I’ll just dump all the cool stuff that’s accumulated on my desktop and bookmark bar here and return to lengthy meandering whenever I don’t feel like I’ve been caught in a bloody tornado 😉

So, here is some Cool Stuff…

(1) A group measured the rate of DNA decay in 158 moa bones of known age from three sites. Really cool stuff, to go out and directly measure how ancient DNA disappears from dead things under more or less identical conditions. The unsurprising result is that DNA decays exponentially, a bit like radioactive material. This suggests that the main cause of the decay is random breaking of the strands. The surprising bit is that this happens much more slowly than previously estimated, suggesting that in ideal (read: frozen) conditions, it might be worth looking for preserved DNA in samples as old as a million years.

(On a side note, if you ever get a chance to see a talk by Eske Willerslev, one of the authors and a leading expert on ancient DNA, don’t miss it. The man is absolutely hilarious.)

(2) The beaks of the finches, ormixing and matching developmental recipes. This study examines the genetic basis of beak shape in three little birds closely related to Darwin’s famous finches. The three finches, just like Darwin’s, share the same basic beak shape, only bigger or smaller. However, there seem to be two distinct developmental programs at work, using different genes and parts of the skeleton to orchestrate beak development. One of the three newly investigated species (the one most closely related to Darwin’s finches) apparently uses the same developmental program as its more famous relatives, even though its beak is shaped more like the other two birds studied here. I told you – genetics, development and homology are complicated 😉

(3) Armoured fossil links worm-like molluscs to chitons. There’s a little-known group (or groups) of molluscs called aplacophorans that have only a coat of tiny spicules instead of shells and look more like worms than “proper” molluscs. Exactly where they fit into our picture of mollusc evolution has been controversial to say the least – they could represent an old lineage separate from other molluscs, they could be related to cephalopods, they could be related to chitons, they could be one group or they could be two lineages in completely different places on the tree… Well, a new fossil named Kulindroplax seems to argue for the chiton connection: the animal has the characteristic armour plates of a chiton on an aplacophoran-like body. Similar creatures have been discovered before, but this guy with its detailed 3D preservation provides the clearest evidence of the link so far.

(4) More cool fossils – this time straight from my beloved Cambrian. Nereocaris, a newly described Burgess Shale arthropod, suggests to its discoverers that the earliest arthropods weren’t predators prowling the seafloor, but swimmers who might have been filter feeders and certainly weren’t predators. The animal has a bivalved shell around its front end, similar to many other Cambrian swimming arthropods, and a long abdomen with paddles at the end. It bears the arthropod hallmark of a hardened and jointed exoskeleton, but it lacks specialised limbs such as antennae or mouthparts. In a cladistic analysis of arthropods and their nearest relatives, the new species comes out on the first branch within true arthropods, and the next few branches as we move towards living arthropods all contain similar shelled, swimming creatures. Since the non-arthropods closest to the real thing (i.e. anomalocaridids) were also fin-tailed swimmers, this arrangement makes the transition between them and true arthropods smoother than previously thought. It also suggests that the hard exoskeleton so characteristic of arthropods originally functioned in swimming – perhaps as an anchor for swimming muscles.

When we talk about evolutionary novelty, especially if the talking is to non-specialists, gene duplication is all the rage. From the sophistication of vertebrate blood clotting to the seemingly pointless complexity of a yeast proton pump (Finnigan et al., 2012), accidentally copied genes are undoubtedly an important source of new stuff in evolution. But copying and tweaking is not the only way new genes can arise. Sometimes, new genes really are new.

I admit, I wasn’t nearly excited enough about this possibility until this paper landed in my RSS reader a while back. Toll-Riera et al. (2012) find that the boring repetitive DNA that my gut feeling would’ve dismissed as true “junk” may actually be a great source of new proteins. First, it’s a good theoretical source . Long stretches of repetitive sequence are less likely than random sequence to suddenly and unceremoniously end in a stop codon* and translate to a short and useless amino acid sequence. Second, it appears that younger proteins do contain more repetitive sequence than old ones. What’s more, the repeats are often found within the regions that confer function on proteins. They aren’t just useless filler.

So, okay, a lot of proteins seem come from pieces of “junk” DNA. How?

Maybe they arise from random gene expression noise and turn into proper genes gradually, say Carvunis et al. (2012). It has been known for a while that DNA that doesn’t belong to traditionally recognised genes quite often gets transcribed into RNA in cells. Sometimes, these random bits of RNA may even be translated into an amino acid chain. If some of these accidents are actually useful, the researchers reasoned, they could create a selection pressure to turn the DNA that produced them into a proper gene.

They took this idea and applied it in a study of open reading frames (ORFs) in the yeast genome. An “ORF” is jargon for a stretch of DNA that isn’t interrupted by stop codons. In theory, any ORF could make a “meaningful” piece of protein. Most ORFs that aren’t genes are short, often just a handful of codons; and most ORFs known to be genes are long, with hundreds of codons. The team argued that if random ORFs can give rise to genes, there should be plenty of transitional forms.

To test this, they first classified all the hundreds of thousands of ORFs in the yeast genome according to their evolutionary age. The ones that were conserved in all of the yeast species they used for comparison were given a score of 10, and ORFs that only brewer’s yeast had were called zeroes. (Most known genes belong to classes 5-10, meaning they evolved quite far back on the yeast family tree.) The next step was to pick the Class Zero ORFs that were actually transcribed and translated, so might be in the pool of potential “proto-genes”. They found this set of “0+” ORFs by analysing RNA sequencing data in both happy yeast cells and yeast deprived of food, just to make sure they caught any sequences that only acted like genes under some circumstances. In addition, they also checked which of those RNAs were associated with ribosomes, the sites of translation. These filtering steps left over a thousand little ORFs that don’t belong to known genes, are completely unique to Saccharomyces cerevisiae, expressed, and probably translated.

Going up the conservation scale, ORFs become increasingly gene-like. The older ones are longer, their RNA copies are more abundant, and more of them appear constrained by natural selection. (Interestingly, when you translate them, the more gene-like ORFs produce less ordered protein structures. Not sure what to make of that.) Proper genes are also better suited to get ribosomes to translate them. Conservation classes 1-4, those ORFs that are shared only by closely related Saccharomyces species, are intermediate in all of these properties (and some more) between the zeroes and the older ORFs.

There is one more thing about this study that definitely bears mentioning When you count how many new gene duplicates this yeast species has versus how many new, potentially functional, random ORFs, the latter come out on top by far. Between them, S. cerevisiae and its closest sister species apparently have somewhere between one and five newly duplicated genes. The same duo also came up with nineteen new ORFs that are under selection and therefore probably functional. Potentially, these random little sequences people might have dismissed as background noise not long ago are more potent sources of new genes than the celebrated gene duplication.

I don’t know about you, but that absolutely fascinates me.

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P.S.: Incidentally, this is all about protein-coding genes. However, thousands of genes in your own genome do NOT encode proteins. They include genes for the good old RNA components of the translation machinery, ribosomal and transfer RNA, but there are also other RNA genes with transcripts involved in everything from keeping parasitic DNA in check to editing the messenger RNAs of other genes. I kind of want to find out how these RNAs form and acquire functions. Also, when we are quite happy to call a piece of DNA that doesn’t have a protein product a “gene”, and cells are swarming with RNA that doesn’t come from things traditionally called “genes”, and some of this RNA actually does encode proteins, what does that do to the definition of a “gene”??

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*Gotta love the mnemonics on that page. I didn’t think three three-letter combinations would be that hard to remember, but I have to admit I chuckled at “U Are Gone”.

“Fishapods” like Tiktaalik and Ichthyostega are among the iconic transitional fossils that mark part of our own evolutionary journey. Understanding how these intriguing animals lived is key to understanding why they ended up out of water, and how evolution took them there. Of course, one of the most important changes that happened to our fishy forebears is gaining the ability to walk. While “walking” may be less of a challenge to fish than we thought, just how good “classical” proto-tetrapods like Ichthyostegawere at it still isn’t entirely clear. (Below: model of Ichthyostega emphasising its aquatic capabilities; photo by Dr Günther Bechly, Wikimedia Commons.)

The recent discovery of tetrapod-like trackways in Mid-Devonian rocks in Poland (Niedźwiedzki et al., 2010) added to the pile of evidence on the “pretty good” side. The footprints appeared to come from feet that looked like those of Ichthyostega, and the trackways betrayed an animal that walked essentially like a modern tetrapod, lifting its body clear off the ground. (The fact that these trackways were left in a different environment and 18 million years earlier than any previously known tetrapod is just the icing.)

As is usually the case in science, the paper wasn’t allowed to be simply right. Using a computerised Ichthyostega skeleton and comparisons to modern tetrapods, Pierce et al. (2012) argue that whatever made the Polish tracks and others like them, it couldn’t have been much like Ichthyostega.

The problem is that Ichthyostega had pretty stiff hip and shoulder joints. The joint surfaces are kind of elongated (and, in the case of the shoulder, also twisted), allowing the bones to hinge in various directions but not to rotate around their long axes. The unrotating hip and rigid knee of the hindlimb made it impossible for the animal to put its soles on the ground. The hindlimb looks very paddle-like with its broad, flattened bones – now it appears that paddling is all it was good for. (Below: a decade of Ichthyostega from Dennis Murphy’s wonderful Devonian Times. See his caption for the sources of the reconstructions.)

By all appearances, Ichthyostega couldn’t rotate its arms and legs enough to walk properly, and couldn’t have left even one of the presumed Polish hindlimb prints without dislocating several joints. The most it could have done is haul itself along like a seal or a mudskipper, which, considering its powerful arms and mobile elbows,might have been exactly what it did. Pierce et al. also argue that other known proto-tetrapods were unlikely to be the trackmakers; while they didn’t examine their limb joints in detail, the skeletons share many of the same features that limit the mobility of Ichthyostega‘s limbs.

That raises plenty of questions. If it wasn’t like any of the known early tetrapods, what sort of creature made those footprints? Were there other ancient tetrapod groups with more limber joints that didn’t leave body fossils because of where they lived? Did the known proto-tetrapods go back to a more aquatic existence and more rigid limbs? (Pierce et al. say that Ichthyostega‘s joints were even stiffer than some of its fishier cousins’!) Which kind begat the lineage that gave rise to living tetrapods? What does all of this say about the significance of walking-like movements we observe in living lobe-finned fish?

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References:

Niedźwiedzki G et al. (2010) Tetrapod trackways from the early Middle Devonian period of Poland. Nature463:43-48